[Numpy-discussion] Problem with libgfortran installed with pip install numpy

David Grote dpgrote at lbl.gov
Mon Nov 12 19:49:40 EST 2018

Yes, thanks, that's something I hadn't looked into. For legacy reasons, my
code was being built with the option -flat_namespace. I don't remember the
reason why, but many years ago that option was needed for the code to run
on the mac. The code is made up of several shared objects that have
dependencies on each other and apparently there was a problem getting it
all linked together properly without that option. But, I tried it out now
without flat_namespace and it seemed to work fine. Whatever the problem
was, it seems to been fixed some other way. It works Ok having the pip
version of numpy (with its old libgfortran).

I'm still curious about why such an old version of gfortran is still being

On Fri, Nov 9, 2018 at 3:09 PM Nathaniel Smith <njs at pobox.com> wrote:

> On Wed, Sep 5, 2018 at 4:37 PM, David Grote <dpgrote at lbl.gov> wrote:
> >
> > Hi - I have recently come across this problem. On my mac, I build a
> Fortran
> > code, producing a shared object, that I import into Python along with
> numpy.
> > This had been working fine until recently when I started seeing sag
> faults
> > deep inside the Fortran code, usually in Fortran print statements. I
> tracked
> > this down to a gfortran version issue.
> >
> > I use the brew installation of Python and gcc (using the most recent
> > version, 8.2.0). gcc of course installs a version of libgfortran.dylib.
> > Doing a lsof of a running Python, I see that it finds that copy of
> > libgfortran, and also a copy that was downloaded with numpy
> >
> (/usr/local/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib).
> > Looking at numpy's copy of libgfortran, I see that it is version 4.9.0,
> much
> > older. Since my code is importing numpy first, the OS seems be using
> numpy's
> > version of libgfortran to link when importing my code. I know from other
> > experience that older versions of libgfortran are not compatible with
> code
> > compiled using a new version of gfortran and so therefore segfaults
> happen.
> Normally on MacOS, it's fine to have multiple versions of the same
> library used at the same time, because the linker looks up symbols
> using a (source library, symbol name) pair. (This is called the
> "two-level namespace".) So it's strange that these two libgfortrans
> would interfere with each other. Does gfortran not use the two-level
> namespace when linking fortran code?
> -n
> --
> Nathaniel J. Smith -- https://vorpus.org
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